A core calculus for the analysis and implementation of biologically inspired languages

The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this thesis we present pi@, an extremely simple and conservative extension of the pi-calculus representing a keystone in this respect, thanks to its expressiveness capabilities. The pi@ calculus is obtained by the addition of polyadic synchronisation and priority to the pi-calculus, in order to achieve compartment semantics and atomicity of complex operations respectively. In its direct application to biological modelling, the stochastic variant of the calculus, Spi@, is shown able to model consistently several phenomena such as formation of molecular complexes, hierarchical subdivision of the system into compartments, inter-compartment reactions, dynamic reorganisation of compartment structure consistent with volume variation. The pivotal role of pi@ is evidenced by its capability of encoding in a compositional way several bio-inspired formalisms, so that it represents the optimal core of a framework for the analysis and implementation of bio-inspired languages. In this respect, the encodings of BioAmbients, Brane Calculi and a variant of P Systems in pi@ are formalised. The conciseness of their translation in pi@ allows their indirect comparison by means of their encodings. Furthermore it provides a ready-to-run implementation of minimal effort whose correctness is granted by the correctness of the respective encoding functions. Further important results of general validity are stated on the expressive power of priority. Several impossibility results are described, which clearly state the superior expressiveness of prioritised languages and the problems arising in the attempt of providing their parallel implementation. To this aim, a new setting in distributed computing (the last man standing problem) is singled out and exploited to prove the impossibility of providing a purely parallel implementation of priority by means of point-to-point or broadcast communication.

Durability of crystalline monumental stones in terms of their petrophysical characteristics

The durability of stone building materials is an issue of utmost importance in the field of monument conservation. In order to be able to preserve our built cultural heritage, the thorough knowledge of its constituent materials and the understanding of the processes that affect them are indispensable. The main objective of this research was to evaluate the durability of a special stone type, the crystalline stones, in correlation with their intrinsic characteristics, the petrophysical properties. The crystalline stones are differentiated from the cemented stones on the basis of textural features. Their most important specific property is the usually low, fissure-like porosity. Stone types of significant monumental importance, like the marble or granite belong to this group. The selected materials for this investigation, indeed, are a marble (Macael marble, Spain) and a granite (Silvestre Vilachán granite, Spain). In addition, an andesite (Szob andesite, Hungary) also of significant monumental importance was selected. This way a wide range of crystalline rocks is covered in terms of petrogenesis: stones of metamorphic, magmatic and volcanic origin, which can be of importance in terms of mineralogical, petrological or physical characteristics. After the detailed characterization of the petrophysical properties of the selected stones, their durability was assessed by means of artificial ageing. The applied ageing tests were: the salt crystallization, the frost resistance in pure water and in the presence of soluble salts, the salt mist and the action of SO2 in the presence of humidity. The research aimed at the understanding of the mechanisms of each weathering process and at finding the petrophysical properties most decisive in the degradation of these materials. Among the several weathering mechanisms, the most important ones were found to be the physical stress due to crystallization pressure of both salt and ice, the thermal fatigue due to cyclic temperature changes and the chemical reactions (mostly the acidic attack) between the mineral phases and the external fluids. The properties that fundamentally control the degradation processes, and thus the durability of stones were found to be: the mineralogical and chemical composition; the hydraulic properties especially the water uptake, the permeability and the drying; the void space structure, especially the void size and aperture size distribution and the connectivity of the porous space; and the thermal and mechanical properties. Because of the complexity of the processes and the high number of determining properties, no mechanisms or characteristics could be identified as typical for crystalline stones. The durability or alterability of each stone type must be assessed according to its properties and not according to the textural or petrophysical classification they belong to. Finally, a critical review of standardized methods is presented, based on which an attempt was made for recommendations of the most adequate methodology for the characterization and durability assessment of crystalline stones.

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Integration of MFA and LCA methodologies: the anthropogenic aluminium cycle in Italy

MFA and LCA methodologies were applied to analyse the anthropogenic aluminium cycle in Italy with focus on historical evolution of stocks and flows of the metal, embodied GHG emissions, and potentials from recycling to provide key features to Italy for prioritizing industrial policy toward low-carbon technologies and materials. Historical trend series were collected from 1947 to 2009 and balanced with data from production, manufacturing and waste management of aluminium-containing products, using a ‘top-down’ approach to quantify the contemporary in-use stock of the metal, and helping to identify ‘applications where aluminium is not yet being recycled to its full potential and to identify present and future recycling flows’. The MFA results were used as a basis for the LCA aimed at evaluating the carbon footprint evolution, from primary and electrical energy, the smelting process and the transportation, embodied in the Italian aluminium. A discussion about how the main factors, according to the Kaya Identity equation, they did influence the Italian GHG emissions pattern over time, and which are the levers to mitigate it, it has been also reported. The contemporary anthropogenic reservoirs of aluminium was estimated at about 320 kg per capita, mainly embedded within the transportation and building and construction sectors. Cumulative in-use stock represents approximately 11 years of supply at current usage rates (about 20 Mt versus 1.7 Mt/year), and it would imply a potential of about 160 Mt of CO2eq emissions savings. A discussion of criticality related to aluminium waste recovery from the transportation and the containers and packaging sectors was also included in the study, providing an example for how MFA and LCA may support decision-making at sectorial or regional level. The research constitutes the first attempt of an integrated approach between MFA and LCA applied to the aluminium cycle in Italy.